Plot holes

Philip and the others are spared at the last second when the machine turns Sugar Plum back into a toy, removing the life from the soldiers she had brought to life. However, there is no explanation as to why this happens. Marie has died and yet all of the people she created in the Four Realms are still alive. Why do the toy soldiers cease to move just because Sugar Plum is gone?

Revealing mistakes

Every decorated conifer has the same silhouette, with an identifiable bare patch on the left side of the trees, suggesting that the image was simply recycled once rendered. Real trees look different from each other.

Spoilers

The goof items below may give away important plot points.

Character error

In the room with the machine which had previously been used to create the toy soldiers, Clara finds a box of "Clockwork Mice" which she uses as a distraction against the soldiers coming after her. Yet she never thinks to use the machine on the mice to create larger ones which could actually fight the soldiers.

Continuity

After Clara's return, stewards collect strings from the gift-giving sequence and wind them up, suggesting that the party has ended. When Clara dances with her father in the gazebo, the estate likewise seems nearly deserted. However, Clara and her family are shown dancing instead in a crowded ballroom moments later. Even earlier, Clara's father indicated that the dancing at the party had been completed.